melting (4.3c-1) debian-dir only changes

Summary

 debian/README.Debian                |   17 ++++++
 debian/README.source                |    4 +
 debian/changelog                    |   99 ++++++++++++++++++++++++++++++++++++
 debian/compat                       |    1 
 debian/control                      |   34 ++++++++++++
 debian/copyright                    |   35 ++++++++++++
 debian/melting-gui.manpages         |    1 
 debian/melting-gui.menu             |    7 ++
 debian/melting.dirs                 |    3 +
 debian/melting.doc-base             |   14 +++++
 debian/melting.docs                 |    4 +
 debian/melting.examples             |    3 +
 debian/melting.install              |    4 +
 debian/melting.manpages             |    1 
 debian/patches/20_fix_manpage.patch |   13 ++++
 debian/patches/series               |    2 
 debian/patches/tkmelting.patch      |   25 +++++++++
 debian/reference                    |   12 ++++
 debian/rules                        |   67 ++++++++++++++++++++++++
 debian/upstream-metadata.yaml       |   21 +++++++
 debian/watch                        |    2 
 21 files changed, 369 insertions(+)

    
download this patch

Patch contents

--- melting-4.3c.orig/debian/melting-gui.menu
+++ melting-4.3c/debian/melting-gui.menu
@@ -0,0 +1,7 @@
+?package(melting-gui):\
+	needs="X11"\
+	section="Applications/Science/Biology"\
+	title="Melting"\
+	command="/usr/bin/tkmelting"\
+	hints="Primer design"\
+	longtitle="Computes the melting temperature for a nucleic acid duplex."
--- melting-4.3c.orig/debian/README.Debian
+++ melting-4.3c/debian/README.Debian
@@ -0,0 +1,17 @@
+Meting for Debian
+─────────────────
+
+Notes about how this package was tested:
+
+After building locally on the developper’s computer, the programs melting and
+tkmelting were briefly tested before uploading the package to the Debian
+archive.
+
+ - melting was ran with the following command line:
+   melting -SAAAAAAAAAAAAAAA -HA -k0.01 -P0.01
+
+ - The tkmelting interface was invoked from the Gnome menu, and the meltin
+   temperature of 0.01 M of the AAAAAAAAAAAAAAA oligonucleotide was calculated
+   for a 0.01 M salt concentration.
+
+ -- Charles Plessy <plessy@debian.org>  Fri, 20 Nov 2009 10:00:28 +0900
--- melting-4.3c.orig/debian/melting-gui.manpages
+++ melting-4.3c/debian/melting-gui.manpages
@@ -0,0 +1 @@
+DOC/tkmelting.1
--- melting-4.3c.orig/debian/reference
+++ melting-4.3c/debian/reference
@@ -0,0 +1,12 @@
+@article{NicolasLe    Novere12012001,
+author = {Le    Novere, Nicolas},
+title = {{MELTING, computing the melting temperature of nucleic acid  duplex}},
+journal = {Bioinformatics},
+volume = {17},
+number = {12},
+pages = {1226-1227},
+doi = {10.1093/bioinformatics/17.12.1226},
+year = {2001},
+URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1226},
+eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/17/12/1226.pdf}
+}
--- melting-4.3c.orig/debian/melting.docs
+++ melting-4.3c/debian/melting.docs
@@ -0,0 +1,4 @@
+DOC/melting
+DOC/melting.html
+DOC/melting.pdf
+README
--- melting-4.3c.orig/debian/control
+++ melting-4.3c/debian/control
@@ -0,0 +1,34 @@
+Source: melting
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy@debian.org>,
+ Andreas Tille <tille@debian.org>
+Build-Depends: debhelper (>= 7), quilt
+Standards-Version: 3.8.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/melting/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/melting/trunk/
+Homepage: http://www.ebi.ac.uk/compneur-srv/melting/
+
+Package: melting
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: melting-gui
+Description: compute the melting temperature of nucleic acid duplex
+ This program computes, for a nucleic acid duplex, the enthalpy, the
+ entropy and the melting temperature of the helix-coil
+ transitions. Three types of hybridisation are possible: DNA/DNA,
+ DNA/RNA, and RNA/RNA. The program first computes the hybridisation
+ enthalpy and entropy from the elementary parameters of each Crick's
+ pair by the nearest-neighbor method. Then the melting temperature is
+ computed. The set of thermodynamic parameters can be easily changed,
+ for instance following an experimental breakthrough.
+
+Package: melting-gui
+Architecture: all
+Depends: perl-tk, melting, ${misc:Depends}
+Description: graphical interface to compute the melting temperature of nucleic acid duplex
+ This package provides a graphical user interface for the “melting”
+ program, which computes for a nucleic acid duplex the enthalpy, the entropy
+ and the melting temperature of the helix-coil transitions.
--- melting-4.3c.orig/debian/melting.manpages
+++ melting-4.3c/debian/melting.manpages
@@ -0,0 +1 @@
+DOC/melting.1
--- melting-4.3c.orig/debian/melting.examples
+++ melting-4.3c/debian/melting.examples
@@ -0,0 +1,3 @@
+BIN/multi.pl
+BIN/profil.pl
+TEST
\ No newline at end of file
--- melting-4.3c.orig/debian/melting.doc-base
+++ melting-4.3c/debian/melting.doc-base
@@ -0,0 +1,14 @@
+Document: melting
+Title: The melting Manual
+Author: Nicolas Le Novère
+Abstract: This manual describes what melting is and how it can be used to
+ compute, for a nucleic acid duplex, the enthalpy, the entropy and the
+ melting temperature of the helix-coil transitions.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/melting/melting.pdf.gz
+
+Format: HTML
+Index: /usr/share/doc/melting/melting.html
+Files: /usr/share/doc/melting/melting/*
--- melting-4.3c.orig/debian/changelog
+++ melting-4.3c/debian/changelog
@@ -0,0 +1,99 @@
+melting (4.3c-1) unstable; urgency=low
+
+  * New upstream release:
+    calls melting from the PATH with its base name (Closes: #549881).
+  * debian/melting/install:
+      multi.pl and profil.pl available in /usr/share/melting.
+  * debian/copyright refreshed to latest experimentations on the format.
+  * Target generating tkmelting manpage removed from debian/rules.
+  * Added various informations about upstream in debian/upstream-metadata.yaml.
+  * Document how to test melting and tkmelting in debian/README.Debian.
+
+ -- Charles Plessy <plessy@debian.org>  Fri, 20 Nov 2009 10:00:28 +0900
+
+melting (4.3b-1) unstable; urgency=low
+
+  Tkmelting did not work in my tests.
+
+  * New upstream release, with new options for Tris, potassium and magnesium
+    concentrations, as well as support for inosine bases.
+
+  [ Charles Plessy ]
+  * debian/control:
+    - Moved bibliographic reference from the long description to a BibTeX file
+      (debian/reference, installed in /usr/share/doc/melting/reference).
+    - Incremented Standards-Version to reflect conformance with Policy 3.8.1
+      (no changes needed).
+    - Improved the description of melting-gui (Closes: #528999).
+    - Dropped versionned build-dependency on quilt (satisfied even in
+      oldstable).
+    - Build-Depend on dephelper 7 (debian/compat set to 7).
+  * debian/rules
+    - NNDIR=/usr/share/melting/NNFILES passed as a make argument instead of
+      through a patch (debian/patches/makefile.patch deleted).
+    - clean target rewritten so that debian/patches/makefile-clean.patch could
+      be deleted.
+    - Use ‘dh’ in binary-arch and binary-indep targets.
+  * Deleted debian/patches/melting.c_silent.patch and
+    debian/patches/melting.1_escape.patch cosmetic deviations from Upstream.
+  * debian/copyright updated and converted to latest version of the
+    machine-readable format.
+  * debian/tkmelting.1* and debian/melting-gui.desktop were adopted upstream and
+    deleted from the debian directory.
+
+  [ David Paleino ]
+  * Removed myself from Uploaders
+
+  [ Andreas Tille ]
+  * debian/control:
+    - Standards-Version: 3.8.3 (Added README.Source)
+    - s/Debian-Med/Debian Med/
+  * debian/patches/20_fix_manpage.patch: Fix typo in manpage
+
+ -- Andreas Tille <tille@debian.org>  Wed, 30 Sep 2009 14:31:20 +0200
+
+melting (4.2h-3) unstable; urgency=low
+
+  * Changed the doc-base section according to the new policy.
+  * Updated my email address.
+
+ -- Charles Plessy <plessy@debian.org>  Sun, 06 Jul 2008 18:11:48 +0900
+
+melting (4.2h-2) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * Moved the Homepage: field out from the package's description.
+  * Debian menu transition: updated debian/melting.doc-base.
+
+  [ David Paleino ]
+  * debian/tkmeltin.1 added - statically built
+  * debian/control:
+    - B-D updated (see above)
+    - added myself to Uploaders
+    - moved XS-Vcs-* to Vcs-*
+  * debian/rules:
+    - manpage statically built
+    - minor changes
+  * Updated to Standards-Version 3.7.3 (no changes needed)
+
+  [ Andreas Tille ]
+  * Added myself to uploaders
+  * debian/melting-gui.manpages: Fixed path to man page
+  * debian/melting.doc-base: Removed extra whitespace
+
+ -- Andreas Tille <tille@debian.org>  Tue, 18 Mar 2008 10:32:48 +0100
+
+melting (4.2h-1) unstable; urgency=low
+
+  * New upstream version: switch to UTF-8 encoding.
+  * Corrects a typo in package description (Closes: #422983).
+  * Debian Menu transition: Apps/Science becomes Applications/Science/Biology.
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Mon, 20 Aug 2007 23:45:32 +0900
+
+melting (4.2g-1) unstable; urgency=low
+
+  * Initial release (Closes: #418691)
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Sun, 22 Apr 2007 11:49:38 +0900
+
--- melting-4.3c.orig/debian/rules
+++ melting-4.3c/debian/rules
@@ -0,0 +1,67 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Build rules for melting. you can use this file without restriction.
+
+# This has to be exported to make some magic below work.
+export DH_OPTIONS
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+	CFLAGS += -O0
+else
+	CFLAGS += -O2
+endif
+
+include /usr/share/quilt/quilt.make
+
+configure: configure-stamp
+configure-stamp:
+	dh_testdir
+	cp makefile.unices Makefile
+	touch $@
+
+build: patch configure build-stamp
+build-stamp:
+	$(MAKE) NNDIR=/usr/share/melting/NNFILES 
+	touch $@
+
+clean: unpatch
+	dh_testdir
+	dh_testroot
+	$(RM) melting.o decode.o calcul.o melting
+	dh_clean build-arch-stamp build-indep-stamp configure-stamp Makefile
+
+install: install-indep install-arch
+install-indep:
+	dh_testdir
+	dh_testroot
+	dh_prep -i 
+	dh_installdirs -i
+	dh_install -i
+	install -D BIN/tkmelting.pl $(CURDIR)/debian/melting-gui/usr/bin/tkmelting
+	install -m 644 -D BIN/melting.hlp  $(CURDIR)/debian/melting-gui/usr/share/melting/melting.hlp
+	install -m 644 -D melting-gui.desktop	$(CURDIR)/debian/melting-gui/usr/share/applications/melting-gui.desktop
+
+install-arch:
+	dh_testdir
+	dh_testroot
+	dh_prep -s 
+	dh_installdirs -s
+#	install melting $(CURDIR)/debian/melting/usr/bin
+	dh_install -s
+
+binary: binary-arch binary-indep
+binary-indep: build install
+	dh binary-indep
+binary-arch: build install-arch
+	dh binary-arch
+
+# This is useful to download the orig.gz sources before running svn-buildpackage
+tarballs:
+	[ -d ../tarballs ] || mkdir ../tarballs
+	uscan --force-download
+	mv ../melt* ../tarballs
+
+binary: binary-arch binary-indep
+.PHONY: build clean binary-indep binary-arch binary install install-indep install-arch configure
--- melting-4.3c.orig/debian/copyright
+++ melting-4.3c/debian/copyright
@@ -0,0 +1,35 @@
+Format: Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
+
+Name: Melting
+Contact: Nicolas Le Novère   <lenov@ebi.ac.uk>
+         Marine Dumousseau  <marine@ebi.ac.uk>
+Source: http://qa.debian.org/watch/sf.php/melting/melting4_3c.tar.gz
+
+Copyright: 1997–2009, Nicolas Le Novère   <lenov@ebi.ac.uk>
+           1997–2009, Marine Dumousseau  <marine@ebi.ac.uk>
+License: GPL-2+
+	
+	Melting is free software; you can redistribute it and/or modify
+	it under the terms of the GNU General Public License as published by
+	the Free Software Foundation; either version 2 of the License, or
+	(at your option) any later version.
+	
+	Melting is distributed in the hope that it will be useful,
+	but WITHOUT ANY WARRANTY; without even the implied warranty of
+	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+	GNU General Public License for more details.
+	
+	You should have received a copy of the GNU General Public License
+	along with this package; if not, write to the Free Software
+	Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+
+On Debian systems, the complete text of the GNU General Public License version
+2 can be found in ‘/usr/share/common-licenses/GPL-2’.
+
+Files: debian/*
+Copyright: 2007–2009  Charles Plessy   <plessy@debian.org>
+             2008     Andreas Tille     <tille@debian.org>
+             2008     David Paleino  <d.paleino@gmail.com>
+License:
+ You can use, redistribute, modify
+ the packaging work as if it were in the public domain.
--- melting-4.3c.orig/debian/upstream-metadata.yaml
+++ melting-4.3c/debian/upstream-metadata.yaml
@@ -0,0 +1,21 @@
+DOI: 10.1093/bioinformatics/17.12.1226
+PubMed: 11751232
+Reference_author: Le Novère, Nicolas
+Reference_title: MELTING, computing the melting temperature of nucleic acid duplex
+Reference_journal: Bioinformatics
+Reference_volume: 17
+Reference_number: 12
+Reference_pages: 1226-1227
+Reference_year: 2001
+Reference_URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1226
+Reference_eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/17/12/1226.pdf
+Reference:
+ author: Le Novère, Nicolas
+ title: MELTING, computing the melting temperature of nucleic acid duplex
+ journal: Bioinformatics
+ volume: 17
+ number: 12
+ pages: 1226-1227
+ year: 2001
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1226
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/17/12/1226.pdf
--- melting-4.3c.orig/debian/README.source
+++ melting-4.3c/debian/README.source
@@ -0,0 +1,4 @@
+This packages uses the quilt patch system. Please read
+/usr/share/doc/quilt/README.source for more information.
+
+ -- Andreas Tille <tille@debian.org>  Wed, 30 Sep 2009 14:31:20 +0200
--- melting-4.3c.orig/debian/melting.install
+++ melting-4.3c/debian/melting.install
@@ -0,0 +1,4 @@
+melting	usr/bin
+NNFILES	usr/share/melting
+BIN/multi.pl	usr/share/melting
+BIN/profil.pl	usr/share/melting
--- melting-4.3c.orig/debian/watch
+++ melting-4.3c/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/melting/melting(.*?)_(.*?)\.tar\.gz
--- melting-4.3c.orig/debian/compat
+++ melting-4.3c/debian/compat
@@ -0,0 +1 @@
+7
--- melting-4.3c.orig/debian/melting.dirs
+++ melting-4.3c/debian/melting.dirs
@@ -0,0 +1,3 @@
+usr/bin
+usr/share/melting
+usr/share/doc/melting
--- melting-4.3c.orig/debian/patches/tkmelting.patch
+++ melting-4.3c/debian/patches/tkmelting.patch
@@ -0,0 +1,25 @@
+Author: Charles Plessy
+Description: Find perl in /usr/bin, and use a different hardcoded path to the help.
+Forwarded: not yet.
+License: same as Melting itself.
+
+Index: melting4_3/BIN/tkmelting.pl
+===================================================================
+--- melting4_3.orig/BIN/tkmelting.pl
++++ melting4_3/BIN/tkmelting.pl
+@@ -1,4 +1,5 @@
+-eval '(exit $?0)' && eval 'exec perl -S $0 ${1+ "$@"}' && eval 'exec perl -S $0 $argv:q' if 0;
++#!/usr/bin/perl
++#eval '(exit $?0)' && eval 'exec perl -S $0 ${1+ "$@"}' && eval 'exec perl -S $0 $argv:q' if 0;
+ 
+ ##############################################################################
+ #                                   MELTING                                  #
+@@ -449,7 +450,7 @@
+ 					     )->pack(-expand => 1,
+ 						     -fill   => 'both'
+ 						   );
+-	open(FH,"melting.hlp") || die "unable to open melting.hlp";
++	open(FH,"/usr/share/melting/melting.hlp") || die "unable to open melting.hlp";
+ 	while (<FH>){
+ 	    $helpText->insert('end', $_);
+ 	}
--- melting-4.3c.orig/debian/patches/20_fix_manpage.patch
+++ melting-4.3c/debian/patches/20_fix_manpage.patch
@@ -0,0 +1,13 @@
+Author: Andreas Tille <tille@debian.org>
+Description: Fix typo in manpage
+--- melting4_3b.orig/DOC/melting.1
++++ melting4_3b/DOC/melting.1
+@@ -55,7 +55,7 @@
+ (SantaLucia et al 1996),
+ .I sug96a.nn
+ (Sugimoto et al 1996)
+-.Isan04a.nn
++.I san04a.nn
+ (Santalucia et al 2004) 
+ (DNA/DNA),
+ .I fre86a.nn
--- melting-4.3c.orig/debian/patches/series
+++ melting-4.3c/debian/patches/series
@@ -0,0 +1,2 @@
+tkmelting.patch
+20_fix_manpage.patch